Despite being given only five minutes to live, ColonelDavid Telford, in the body of Dr.Nicholas Rush, continues to resist. As he runs out of air, Camile Wray grabs Lt.Matthew Scott's radio and tries to convince Dr.Adam Brody to restore life support, since he will murder both Telford and Rush otherwise. ColonelEverett Young orders him to disregard the request. Scott begins to argue in Telford's favor, but Young insists that he knows what he's doing, and Greer pushes Scott back when he attempts to intervene. Telford begins to asphyxiate, and same happens to Rush in Telford's body. Young counts down on his watch, then has Brody restore air to the room. Young resuscitates Telford, breaking him free of the brainwashing. Telford reveals that the Lucian Alliance is coming to take Destiny.

Young explains the situation to the crew. The gate room is sealed and all nearby corridors are put under guard. The civilians are told to stay in their quarters if and when the invasion occurs. Homeworld Command has been informed of the location of the Lucian Alliance base, and if they're lucky it will be captured before the invasion occurs. Otherwise they'll be on their own, but Young assures the crew that it will be dealt with quickly. Wray confronts Young about his sudden trust in Telford, but he brushes her off. Scott insists that he should have been told that killing and reviving Telford would break the brainwashing, but Young simply states that he does not have to explain every order he gives. He visits Telford in the infirmary and they reconcile their differences, since the brainwashing is what made Telford so confrontational. Telford asks Young to shut off the stones so they he can help on the other side, but Young wants him to recover first. Young then speaks to Lt.Tamara Johansen, asking her to stay back in case the Alliance breaks out of the gate room. She'll be needed to treat the wounded. He explains that he plans to vent the atmosphere in the room once the Alliance arrives.

Rush awakens in Telford's body with a large cut on his hand. CommanderKiva wanted to make sure he wasn't faking his near-death experience. ColonelSamantha Carter arrives over the planet in the George Hammond. The facility is shielded against beaming, so she dispatches a squadron of F-302 fighter-interceptor's for a ground assault. As the attack begins, Kiva wants to know if they can dial Destiny. Rush confirms that they can, but doing so will destroy the planet. Kiva orders it done. Her group evacuates through the gate with Rush in tow. Carter is forced to leave the area before the planet explodes; two F-302's are lost.

On Destiny, Eli Wallace is watching Dr.Daniel Jackson's video on the Lucian Alliance from the Kino room. He is joined by Chloe Armstrong. Destiny drops out of FTL to receive the incoming wormhole. As the Alliance forces come in, Young prepares to vent the atmosphere, but hesitates when Rush is among those in the gate room. He decides to try a diplomatic approach instead. The communication stone link has been broken by their trip through the gate, so it is actually Telford. Kiva holds him at gunpoint, still believing him to be Rush, and blames him for the deaths of over 100 of her men. Telford tells Kiva her father's name, Masim, as proof of his identity so she'll stand down. Over the intercom, Young informs the Alliance forces that they are surrounded and locked in, and that he can vent the atmosphere at any time. He demands they lower their weapons. Kiva has Telford confirm that Young can do this, then has her men open the doors using devices which override the locks. The Alliance forces move out from the gate room and begin their assault on the crew. Rush heads for the control room, followed by TJ. In the ensuing firefight, four Alliance officers are captured by the Destiny crew while ten of their people are caught by the Alliance, with TJ, Sgt.Hunter Riley, and Cpl.Rivers among them.

Eli and Chloe, having stayed in the Kino room, are forced to use an elevator to escape the attacking Alliance forces, ending up in a different area of the ship. Chloe has a gunshot wound on her leg. They are assumed captured by the rest of the crew. Eli has no idea where they are, having randomly entered a destination. They cannot get back, either, since the elevators have been locked down. Instead, they will have to make their way back on foot. Since Chloe can't walk by herself, Eli supports her.

In the control room, Rush asks why Young didn't vent the compartment immediately. Dr.Dale Volker claims it was to save Rush, but Rush states that he was switched back as soon as he came through the gate. Young asks for an overview of the situation. The Alliance has taken the gate room and the surrounding corridors. They've stopped so as to avoid overextending themselves, but with their technology no door locks are going to stop them. Likewise, any attempt to overrun them will immediately result in the death of the hostages.

Kiva radios Young, informing him that she has no intention of surrendering. She claims to want the same thing as the Destiny crew, and promises to allow them to remain on board or disembark on a habitable planet if they surrender to her. Young responds that he can still vent the atmosphere on Kiva's side. Kiva insists that he'd have done it already if he had the nerve, but Young merely reiterates that he can. Kiva decides to execute TJ, Riley, and Rivers to show that she's serious, but Telford dissuades her, arguing that it will force Young's hand. He instead proposes an alternate plan that will get them around the blockade and into the Control interface room by cutting through into one of the damaged sections. Kiva sends him to complete the mission, with the threat that the hostages will die should he fail.

Camile is escorted in by MSgt.Ronald Greer. She wants to negotiate since the situation is no longer possible to swiftly resolve, and believes she should do the talking. Camile radios Kiva and tells her that while they won't relinquish control of the ship, they will propose a hostage trade, four for four, allowing Kiva to regain her men while not sacrificing all her hostages. Kiva will consider it. This will buy some time for Young to prepare a plan. Once their conversation is done, Rush argues that the situation only has one possible outcome. The Alliance members will never give up their hostages, and sooner or later they will need to be sacrificed to resolve the situation. Young, however, is adamant about saving everyone. Since Telford is among the Alliance forces, they have a chance of catching them by surprise. Rush rhetorically asks if they are to trust a traitor with the ship and the lives of the entire crew.

Eli and Chloe find a window, learning that the elevator has taken them near the bow of the ship. Chloe notes that the air seems to be getting thin, and Eli confirms that the life support isn't working in this section, since he shut it down himself on Rush's orders. The section is pressurized, but the air isn't being recycled. Chloe collapses when she tries to move away from the railing by the window, and can no longer stand. Eli carries her in his arms.

Kiva has TJ treat Varro, her wounded lieutenant. TJ tells her that he's badly wounded. Meanwhile, Young uses the communication stones to inform Lt. GeneralJack O'Neill of the situation. O'Neill dresses him down for hesitating, stating that the situation should have been resolved on the spot. He uses Carter's necessary abandonment of the F-302's lost in the raid on the Lucian Alliance planet as a comparison, and informs Young that if he can't resolve the situation, he can have someone replace Young to do it. Young assures O'Neill that he will not let the ship fall to the Alliance. In the control room, Rush realizes that the jump countdown is blank, even though they should have gone to FTL almost immediately.

After cutting a hole through a nearby wall, Telford leads his group through the ship. He stops to activate a panel to check their position, alerting Young to his activities. They come to one of the sealed doors, and an Alliance officer prepares to open it. However, before he can set the door override device, the part of the shield covering a hull breach above the door begins to radiate with intense blue light. The man spontaneously combusts. Power all over the ship suddenly fluctuates. When it passes, Telford opens the door and asks if Young was responsible. Young confirms he wasn't, and they decide to wait for another opportunity to stop the Alliance forces. Telford asks for a radio, and tells Young that to switch to channel 6 on three clicks. He closes the door and heads back.

Elsewhere, Eli is starting to get tired from carrying Chloe, though he tries to claim he's fine. He brags about climbing a mountain once, but under questioning admits it was actually in the video game World of Warcraft. They decide to rest. Chloe wonders why no one's come looking for them, and if the invasion has been stopped. Eli jokingly goes over the things that need to happen first, such as a celebratory party. Chloe is getting tired, and Eli explains that she's still losing blood. He assures her that he will take care of her.

Kiva confronts Young about the death of her soldier, and he tells her that it was a random occurrence. As a show of good faith, she requests medical supplies. Camile sees this as a harmless gesture, but Rush argues otherwise: there will come a point when desperation overwhelms reason in the Alliance officers, and when that happens the hostages will die. Young agrees, planning to end the situation immediately.

Young: How you feeling, David? Telford: Confused. Young: I bet. Telford: You went the whole nine yards. To the brink and back. Young: I had to. You know in my defense, it wasn't the first thing I tried. Telford: Yeah, thanks for that. Young: At least the brainwashing explains why you've been such an ass.

Carter: Sir, it looks like the intel is good. The planet's laced with naquadria deposits. We're also reading a huge energy signature emanating from what looks like a pyramid. O'Neill: Pyramid? That takes me back.

(Eli is carrying Chloe)Chloe: Let's stop.Eli: Huh? I'm fine.Chloe: Eli.Eli: Seriously, this is nothing. Once, I climbed the Red Ridge Mountains, on my way to Stonard, with a full pack.Chloe: Where's that?Eli:World of Warcraft.Chloe: Wow. That must've given you quite the sense of accomplishment.

Chloe: So what do you think is happening? Eli: Probably won by now. Chloe: You think so? (Eli shrugs) If we won, then why haven't we been rescued? Eli: Well, first they have to figure out what to do with the prisoners; and then there's that whole post-victory celebration. I mean, streamers everywhere.

This is the second time that dialing Destiny while under attack has destroyed an entire planet.

Due to the power surge generated by the explosion of a planet, travelers were thrown out of the Destiny gate at high velocity. As the gate has never been dialed under less extreme conditions, it is unknown if this is merely a side effect of dialing such a long distance.

"Incursion" was originally slated to be a single episode, but while writing it, Joe Mallozzi began to realize it would have to be longer. There were initial concerns it would be three parts, with the third part airing as the season two premiere, but after various edits, it was tightened to two episodes. "Subversion", originally slated to be the 19th and penultimate episode of season one, became the 18th episode and the previous episode, "Pain", aired as the 17th.

Kiva, like Young in "Air, Part 1", instructs the first wave of insurgents to radio back once they've arrived aboard Destiny, unbeknownst to her the distance of a nine-chevron address is so great it does not allow for the two-way radio communication that gate travelers are accustomed to with shorter distances.